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Literature summary extracted from

  • Gogoi, P.; Mordina, P.; Kanaujia, S.P.
    Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase (2019), J. Struct. Biol., 205, 67-77 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
5.3.1.23 Orf PH0702, sequence comparisons and phylogenetic tree, recombinant expression of His-tagged enzyme in Escherichia coli strain Rosetta(DE3) Pyrococcus horikoshii

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
5.3.1.23 purified recombinant enzyme in two different forms of crystals belonging to space groups P3221 and P1, that are obtained at 4°C and 20°C, respectively. The crystal belonging to space group P3221 grows in a microbatch-under-oil set up by mixing 0.002 ml of protein solution and 0.002 ml of 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 2.5 M 1,6-hexanediol. Initial crystals belonging to space group P1 are obtained by hanging-drop vapor-diffusion method, mixing of 0.003 ml of protein solution with 0.001 ml of resevoir solution containing 0.05 M ammonium acetate, 0.1 M Tris, pH 8.0, 16% PEG 10000 and 0.05 M sodium acetate, method optimization, X-ray diffraction structure determination analysis at 2.30-2.65 A resolution, molecular replacement method using the three-dimensional atomic coordinates of M1Pi from Archaeoglobus fulgidus (PDB ID 1T5O) as the search model, modeling Pyrococcus horikoshii

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
5.3.1.23 80000
-
 about, recombinant enzyme, native PAGE Pyrococcus horikoshii

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
5.3.1.23 S-methyl-5-thio-alpha-D-ribose 1-phosphate Pyrococcus horikoshii
-
 S-methyl-5-thio-D-ribulose 1-phosphate
-
 r

Organism

EC Number Organism UniProt Comment Textmining
5.3.1.23 Pyrococcus horikoshii O58433
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
5.3.1.23 recombinant His-tagged enzyme from Escherichia coli strain Rosetta(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration Pyrococcus horikoshii

Reaction

EC Number Reaction Comment Organism Reaction ID
5.3.1.23 S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate catalytic reaction mechanism, structure-function relationship, overview. Proposed reaction mechanism of M1Pi proceeds via a cis-phosphoenolate intermediate and through the following steps: (1) transfer of proton from Asp247 to the O4 atom of MTR-1-P, (2) proton abstraction from C2 atom of the substrate by the thiolate anion of Cys167 as well as cleavage of the C1-O4 bond, (3) simultaneous proton abstraction from O2 atom by the deprotonated Asp247 and transfer of proton from the thiol group of Cys167 to C1 atom, and (4) generation of the product, MTRu-1-P Pyrococcus horikoshii
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
5.3.1.23 S-methyl-5-thio-alpha-D-ribose 1-phosphate
-
 Pyrococcus horikoshii S-methyl-5-thio-D-ribulose 1-phosphate
-
 r

Subunits

EC Number Subunits Comment Organism
5.3.1.23 homodimer 2 * 40000, about, recombinant enzyme, SDS-PAGE Pyrococcus horikoshii
5.3.1.23 More enzyme three-dimensional structure analysis and structure comparisons. The most visible difference between the open and closed conformation can be perceived in the position of the loop connecting the helices alpha3 and alpha4 of the NTD. In the open state, the loop is away from the active-site pocket, whereas in the closed state the loop moves toward the active-site pocket with a forward shift of about 24 A Pyrococcus horikoshii

Synonyms

EC Number Synonyms Comment Organism
5.3.1.23 5-methylthioribose 1-phosphate isomerase
-
 Pyrococcus horikoshii
5.3.1.23 PH0702 locus name Pyrococcus horikoshii
5.3.1.23 PhM1Pi
-
 Pyrococcus horikoshii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
5.3.1.23 8
-
 assay at Pyrococcus horikoshii

General Information

EC Number General Information Comment Organism
5.3.1.23 evolution the enzyme is a member of the family PF01008. The open and closed states of the proteins belonging to the family PF01008 are usually demarcated by the degree of angle formed owing to the bend in the longest helix alpha5 Pyrococcus horikoshii
5.3.1.23 additional information transition from an open to closed state creates a hydrophobic active site environment. The active-site pocket of M1Pi is optimized to follow a reaction mechanism via the formation of a cis-phosphoenolate intermediate, structural transition, overview Pyrococcus horikoshii